Henry McLeish said in his long-awaited report into the future of sport, the focus should be on the smooth transition from Team GB for those sportsmen and women who wish to compete for Scotland.
The games will take place in August 2016, some four months after the proposed date for Scottish independence.
Mr McLeish said any participation would still be subject to an application meeting the International Olympic Committee's timetable.
He wrote in the 53-page document: "There is a well-established application process and no obvious barriers to Scotland participating in the Olympics or Para-Olympics.
"By putting athletes' needs first there are opportunities to build on the support already in place for international athletes to develop a successful Team Scotland on the Olympic and Paralympic stage."
Six-time Olympic gold medal winning former cyclist Sir Chris Hoy has been critical of attempts to create a separate Scotland team. The Edinburgh-born Team GB star said in 2012 it is possible to compete as both "Scottish and British" in the Olympics,
The report, titled: 'The continuing development of Scottish Sport - including the impact of Independence' published last night also called for more effort to ensure communities and schools benefit from "substantial" improvements to sports facilities.
The document said effort is required to ensure all groups, especially those in the most deprived areas, benefit from new and existing assets.
It also said Scotland's over-complicated sports governance and funding structures need to be simplified.
Mr McLeish called for the Government to consider future spending as a cost saving exercise against health and other budgets.
Among other recommendations, the report said the national agency, sportscotland needs to better understand the role and levels of coaching.
l Labour have called on Foreign Secretary William Hague to ensure that the Commonwealth Games in Glasgow are not overshadowed by protests over the presence of the president of Sri Lanka. Mahinda Rajapaksa's regime is accused of committing human rights abuses.